Samantha A. Morris

This study shows that clonal memory in human embryonic stem cells influences fate potential during endoderm differentiation by heritable chromatin states.

This study shows that adipocytes are not essential for ovarian cancer growth in the omentum, but endothelial FABP4 plays a critical role in supporting tumor metabolic growth.

The paper uses single-cell RNA sequencing to identify new adipocyte precursor populations and reveals Sox9's role in adipose commitment.

The paper uses CellOracle to analyze GRN reconfiguration during fibroblast to iEP reprogramming, identifying Fos and Yap1 as key factors for successful conversion.

The paper introduces CellTag-multi, a method for multiomic single-cell lineage tracing that combines chromatin accessibility with lineage barcodes, and applies it to study reprogramming outcomes and gene regulatory programs in mouse hematopoiesis.

The paper defines the cellular and transcriptional features of cardiac recovery using snRNA-seq, identifying RUNX1 downregulation as a key predictor and potential therapeutic target.

Capybara measures cell identity and fate transitions using a continuum-based approach, showing improved performance in annotating cells and identifying transitions in hematopoiesis and reprogramming.

This study profiles transcriptional and morphogenetic features of human gastruloids, identifying seven cell types and conserved sorting behaviors during embryogenesis.

This paper introduces self-reporting transposons (SRTs) and the scCC assay to simultaneously capture gene expression and TF binding in single cells, demonstrating their use in cultured cells and mouse cortex.

Gene regulatory networks inferred from single-cell transcriptome and epigenome data are perturbed in silico to predict transcription-factor perturbation outcomes and to nominate factors that raise reprogramming yield.

CellTag Indexing enables genetic barcode-based multiplexing for single-cell genomics, allowing simultaneous sample identification and transcriptional analysis across diverse cell types.

The paper uses single-cell RNA sequencing to show that mice adapt to small bowel resection by reprogramming distal intestinal enterocytes to a proximal identity, driven by retinoid metabolism and Creb3l3.

This paper introduces a lineage-tracing method called CellTagging to study clonal dynamics in direct lineage reprogramming from fibroblasts to induced endoderm progenitors, revealing rare successful reprogramming events and clonal instability.

The paper compares kidney organoid and adult human kidney single-cell and single-nucleus transcriptomes to assess differentiation maturity and identify transcription factor networks.